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Conference Papers Year : 2018

Fixed-Parameter Tractable Sampling for RNA Design with Multiple Target Structures

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Abstract

The design of multi-stable RNA molecules has important applications in biology, medicine, and biotechnology. Synthetic design approaches profit strongly from effective in-silico methods, which can tremendously impact their cost and feasibility. We revisit a central ingredient of most in-silico design methods: the sampling of sequences for the design of multi-target structures, possibly including pseudoknots. For this task, we present the efficient, tree decomposition-based algorithm \ourprog{}. Our fixed parameter tractable approach is underpinned by establishing the $\#${\sf P}-hardness of uniform sampling. Modeling the problem as a constraint network, \ourprog{} supports generic Boltzmann-weighted sampling for arbitrary additive RNA energy models; this enables the generation of RNA sequences meeting specific goals like expected free energies or \GCb-content. Finally, we empirically study general properties of the approach and generate biologically relevant multi-target Boltzmann-weighted designs for a common design benchmark. Generating seed sequences with \ourprog{}, we demonstrate significant improvements over the previously best multi-target sampling strategy (uniform sampling).Our software is freely available at: https://github.com/yannponty/RNARedPrint .
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Dates and versions

hal-01631277 , version 1 (09-11-2017)
hal-01631277 , version 2 (31-03-2018)

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Stefan Hammer, Yann Ponty, Wei Wang, Sebastian Will. Fixed-Parameter Tractable Sampling for RNA Design with Multiple Target Structures. RECOMB - 22nd Annual International Conference on Research in Computational Molecular Biology - 2018, Apr 2018, Paris, France. ⟨hal-01631277v2⟩
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